19-35288519-C-G

Variant names:

• chr19-35288519-C-G
• rs12971321

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.577 in 151,738 control chromosomes in the GnomAD database, including 25,738 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (25738 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87431 AN: 151620 Hom.: 25730 Cov.: 29

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.615

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.577 AC: 87482 AN: 151738 Hom.: 25738 Cov.: 29 AF XY: 0.576 AC XY: 42745 AN XY: 74156

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.611

Alfa AF: 0.479 Hom.: 1345

Bravo AF: 0.570

Asia WGS AF: 0.514 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12971321; hg19: chr19-35779422;